Class QsAlignResult
- java.lang.Object
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- org.biojava.nbio.structure.align.quaternary.QsAlignResult
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public class QsAlignResult extends Object
Result of a Quaternary Structure AlignmentQsAlign
. The QsAlignResult holds the original inputs of the algorithm and the results and scores of the alignment.- Since:
- 5.0.0
- Author:
- Aleix Lafita
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Atom[]
getAlignedAtomsForSubunits1(int index)
Atom[]
getAlignedAtomsForSubunits2(int index)
List<Subunit>
getAlignedSubunits1()
Return the aligned subunits of the first Subunit group, in the alignment order.List<Subunit>
getAlignedSubunits2()
Return the aligned subunits of the second Subunit group, in the alignment order.MultipleAlignment
getAlignment()
The alignment that specifies the residue equivalencies of the equivalent Subunits.QsRelation
getRelation()
The quaternary structure relationQsRelation
between the two groups of Subunits.double
getRmsd()
The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups.Map<Integer,Integer>
getSubunitMap()
Map of Subunit equivalencies from the first to the second group.List<Subunit>
getSubunits1()
Original Subunits of the first group.List<Subunit>
getSubunits2()
Original Subunits of the second group.javax.vecmath.Matrix4d
getTransform()
The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.int
length()
The length of the alignment is the number of Subunit equivalencies it contains.void
setAlignment(MultipleAlignment alignment)
The alignment that specifies the residue equivalencies of the equivalent Subunits.void
setClusters(List<SubunitCluster> clusters)
void
setRelation(QsRelation relation)
The quaternary structure relationQsRelation
between the two groups of Subunits.void
setSubunitMap(Map<Integer,Integer> subunitMap)
Map of Subunit equivalencies from the first to the second group.String
toString()
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Method Detail
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getSubunits1
public List<Subunit> getSubunits1()
Original Subunits of the first group.- Returns:
- an unmodifiable view of the original List
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getSubunits2
public List<Subunit> getSubunits2()
Original Subunits of the second group.- Returns:
- an unmodifiable view of the original List
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getSubunitMap
public Map<Integer,Integer> getSubunitMap()
Map of Subunit equivalencies from the first to the second group.- Returns:
- an unmodifiable view of the original Map
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setSubunitMap
public void setSubunitMap(Map<Integer,Integer> subunitMap)
Map of Subunit equivalencies from the first to the second group.- Parameters:
subunitMap
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length
public int length()
The length of the alignment is the number of Subunit equivalencies it contains. This is equivalent to the size of the Subunit Map.- Returns:
- length of the alignment
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getTransform
public javax.vecmath.Matrix4d getTransform()
The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.This is equivalent to multipleAlignment.getBlockSet(0).getTransformations().get(1).
- Returns:
- Matrix4d
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getRmsd
public double getRmsd()
The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups. This is equivalent to multipleAlignment.getScore(MultipleAlignmentScorer.RMSD).- Returns:
- rmsd
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getRelation
public QsRelation getRelation()
The quaternary structure relationQsRelation
between the two groups of Subunits.- Returns:
- relation
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setRelation
public void setRelation(QsRelation relation)
The quaternary structure relationQsRelation
between the two groups of Subunits.- Parameters:
relation
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getAlignment
public MultipleAlignment getAlignment()
The alignment that specifies the residue equivalencies of the equivalent Subunits.- Returns:
- alignment as a MultipleAlignment object
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setAlignment
public void setAlignment(MultipleAlignment alignment)
The alignment that specifies the residue equivalencies of the equivalent Subunits.- Parameters:
alignment
- a MultipleAlignment object
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getAlignedSubunits1
public List<Subunit> getAlignedSubunits1()
Return the aligned subunits of the first Subunit group, in the alignment order.- Returns:
- a List of Subunits in the alignment order
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getAlignedSubunits2
public List<Subunit> getAlignedSubunits2()
Return the aligned subunits of the second Subunit group, in the alignment order.- Returns:
- a List of Subunits in the alignment order
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setClusters
public void setClusters(List<SubunitCluster> clusters)
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getAlignedAtomsForSubunits1
public Atom[] getAlignedAtomsForSubunits1(int index)
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getAlignedAtomsForSubunits2
public Atom[] getAlignedAtomsForSubunits2(int index)
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